Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
Robert Aboukhalil
Johannes Köster
New work on using transformers (using gene order) for tasks in genomic epidemiology:
www.biorxiv.org/content/10.6...
We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
Thank you very much to the folks at Seqera for the opportunity to speak about new adventures in Bactopia.
Haha you'll have to wait for the video for the jokes, but for now the slides are available here: bactopia.io/impact-and-o...
A curated Collection of Bactopia related Talks and Posters.
@lfeatherstone.bsky.social and I have just released v1.10.2 of clockor2.github.io 🎉 including several performance upgrades. Here we reproduce the results of McBride et al 2023, showing accelerated evolution of SARS-CoV-2 in white-tailed deer transmission clusters 🦌🦠
go.unimelb.edu.au/ydo2
At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa....
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa....
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
Robert Petit
John Lees
New feature for PearTree - root-to-tip plots. Web version at peartree.live | desktop apps to follow at github.com/artic-network/peartree/releases/latest
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
Very happy to see Wasm gaining traction as a low barrier to entry alternative for programming thanks to the massive efforts by @quantstack.bsky.social 🎉 We're collecting Wasm resources for bioinformatics and beyond at wasmodic.github.io
Enjoying the little things like antibodies, ion channels and pip installs - technical biologist building tools and studying diseases ❤️🐢
